Mercurial > repos > bgruening > text_processing

annotate find_and_replace.xml @ 26:f22a309187a3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
author bgruening
date Fri, 16 Aug 2024 10:41:17 +0000
parents cd83b5644eab
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
26
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
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1 <tool id="tp_find_and_replace" name="Replace" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>parts of text</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7 <requirements>
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8 <requirement type="package" version="5.32">perl</requirement>
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9 </requirements>
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10 <command>
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11 <![CDATA[
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12 #for $i, $el in enumerate($find_and_replace)
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13 #if $i == (len($find_and_replace) - 1)
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14 #set $join = ""
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15 #else
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16 #set $join = "|"
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17 #end if
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18 perl '$__tool_directory__/find_and_replace'
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19 #if $el.searchwhere.searchwhere_select == "column":
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20 -c $el.searchwhere.column
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21 #end if
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22 #if $i == (len($find_and_replace) - 1)
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23 -o '$outfile'
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24 #end if
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25 $el.global
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26 $el.caseinsensitive
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27 $el.wholewords
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28 $el.skip_first_line
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29 $el.is_regex
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30 '$el.find_pattern'
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31 '$el.replace_pattern'
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32 #if $i == 0
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33 '$infile'
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34 #end if
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35 $join
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36 #end for
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37 ]]>
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38 </command>
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39 <inputs>
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40 <param name="infile" format="txt" type="data" label="File to process" />
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41 <repeat name="find_and_replace" title="Find and Replace" min="1">
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42 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
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43 <sanitizer>
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44 <valid initial="string.printable">
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45 <remove value="&apos;"/>
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46 </valid>
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47 </sanitizer>
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48 </param>
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49 <param name="replace_pattern" type="text" label="Replace with"
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50 help="Use simple text, or $&amp; (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." >
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51 <sanitizer>
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52 <valid initial="string.printable">
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53 <remove value="&apos;"/>
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54 </valid>
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55 </sanitizer>
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56 </param>
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57 <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue=""
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58 label="Find-Pattern is a regular expression" help="see help section for details." />
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59
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60 <param name="global" type="boolean" checked="false" truevalue="-g" falsevalue=""
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61 label="Replace all occurences of the pattern" />
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62
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63 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue=""
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64 label="Case-Insensitive search" help="" />
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65
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66 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue=""
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67 label="Find whole-words" help="ignore partial matches (e.g. 'apple' will not match 'snapple')" />
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68
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69 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue=""
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70 label="Ignore first line" help="Select this option if the first line contains column headers. Text in the line will not be replaced. " />
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71
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72 <conditional name="searchwhere">
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73 <param name="searchwhere_select" type="select" label="Find and Replace text in">
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74 <option value="line" selected="true">entire line</option>
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75 <option value="column">specific column</option>
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76 </param>
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77 <when value="line" />
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78 <when value="column">
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79 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
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80 </when>
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81 </conditional>
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82 </repeat>
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83 </inputs>
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84 <outputs>
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85 <data format_source="infile" name="outfile" metadata_source="infile" />
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86 </outputs>
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87 <tests>
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88 <test expect_num_outputs="1">
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89 <param name="infile" value="find_and_replace1.txt" />
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90 <repeat name="find_and_replace">
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91 <param name="find_pattern" value="day" />
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92 <param name="replace_pattern" value="great day" />
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93 <param name="is_regex" value="False" />
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94 <param name="global" value="true" />
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95 <param name="caseinsensitive" value="False" />
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96 <param name="wholewords" value="True" />
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97 </repeat>
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98 <output name="outfile" file="find_and_replace_results1.txt" />
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99 </test>
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100 <!-- test that columns are split by tab not space. input has no tab loads of spaces
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101 .. therefore the ftype needs to be set.
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102 result should be the same as in test 1 which works on whole line -->
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103 <test expect_num_outputs="1">
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104 <param name="infile" value="find_and_replace1.txt" ftype="tabular" />
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105 <repeat name="find_and_replace">
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106 <param name="find_pattern" value="day" />
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107 <param name="replace_pattern" value="great day" />
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108 <param name="is_regex" value="False" />
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109 <param name="global" value="true" />
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110 <param name="caseinsensitive" value="False" />
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111 <param name="wholewords" value="True" />
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112 <conditional name="searchwhere">
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113 <param name="searchwhere_select" value="column"/>
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114 <param name="column" value="1" />
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115 </conditional>
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116 </repeat>
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117 <output name="outfile" file="find_and_replace_results1.txt" />
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118 </test>
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119 <test expect_num_outputs="1">
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120 <param name="infile" value="find_and_replace2.txt" />
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121 <repeat name="find_and_replace">
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122 <param name="find_pattern" value="^chr" />
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123 <param name="replace_pattern" value="" />
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124 <param name="is_regex" value="True" />
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125 <param name="caseinsensitive" value="False" />
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126 <param name="wholewords" value="False" />
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127 <conditional name="searchwhere">
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128 <param name="searchwhere_select" value="column" />
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129 <param name="column" value="3" />
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130 </conditional>
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131 </repeat>
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132 <output name="outfile" file="find_and_replace_results2.txt" />
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133 </test>
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134 <test expect_num_outputs="1">
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135 <param name="infile" value="find_and_replace1.txt" />
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136 <repeat name="find_and_replace">
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137 <param name="find_pattern" value="day" />
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138 <param name="replace_pattern" value="great day" />
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139 <param name="is_regex" value="False" />
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140 <param name="global" value="true" />
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141 <param name="caseinsensitive" value="False" />
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142 <param name="wholewords" value="True" />
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143 </repeat>
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144 <param name="infile" value="find_and_replace1.txt" />
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145 <repeat name="find_and_replace">
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146 <param name="find_pattern" value="great" />
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147 <param name="replace_pattern" value="best" />
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148 <param name="is_regex" value="False" />
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149 <param name="global" value="False" />
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150 <param name="caseinsensitive" value="False" />
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151 <param name="wholewords" value="True" />
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152 </repeat>
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153 <output name="outfile" file="find_and_replace_results3.txt" />
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154 </test>
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155 </tests>
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156 <help>
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157 <![CDATA[
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158 **What it does**
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159
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160 This tool finds $ replaces text in an input dataset.
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161
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162 .. class:: infomark
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163
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164 The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box).
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165
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166 .. class:: infomark
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167
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168 When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 )
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169
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170 .. class:: infomark
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171
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172 This tool uses `Perl regular expression <https://perldoc.perl.org/perlre>`_ syntax.
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173
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174 -----
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175
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176 **Examples of *regular-expression* Find Patterns**
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177
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178 - **HELLO** The word 'HELLO' (case sensitive).
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179 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
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180 - **A{4,}** Four or more consecutive A's.
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181 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
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182 - **hsa-mir-([^ ]+)** The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern.
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183
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184
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185 **Examples of Replace Patterns**
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186
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187 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
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188 - **FOO-$&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$&** (dollar-ampersand) represents the matched find pattern.
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189 - **$1** The text which matched the first parenthesis in the Find Pattern.
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190
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191
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192 -----
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193
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194 **Example 1**
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195
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196 **Find Pattern:** HELLO
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197 **Replace Pattern:** WORLD
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198 **Regular Expression:** no
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199 **Replace what:** entire line
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200
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201 Every time the word HELLO is found, it will be replaced with the word WORLD.
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202
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203 -----
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204
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205 **Example 2**
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206
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207 **Find Pattern:** ^chr
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208 **Replace Pattern:** (empty)
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209 **Regular Expression:** yes
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210 **Replace what:** column 11
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211
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212 If column 11 (of every line) begins with ther letters 'chr', they will be removed. Effectively, it'll turn "chr4" into "4" and "chrXHet" into "XHet"
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213
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214
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215 -----
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216
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217 **Perl's Regular Expression Syntax**
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218
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219 The Find & Replace tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.
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220
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221 - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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222 - **^** matches the beginning of a string(but not an internal line).
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223 - **(** .. **)** groups a particular pattern.
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224 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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225
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226 - **{n}** The preceding item is matched exactly n times.
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227 - **{n,}** The preceding item ismatched n or more times.
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228 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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229
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230 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
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231 - **.** Matches any single character except a newline.
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232 - ***** The preceding item will be matched zero or more times.
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233 - **?** The preceding item is optional and matched at most once.
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234 - **+** The preceding item will be matched one or more times.
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235 - **^** has two meaning:
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236 - matches the beginning of a line or string.
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237 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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238 - **$** matches the end of a line or string.
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239 - **\\|** Separates alternate possibilities.
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240 - **\\d** matches a single digit
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241 - **\\w** matches a single letter or digit or an underscore.
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242 - **\\s** matches a single white-space (space or tabs).
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243
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244 ]]>
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245 </help>
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7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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246 <expand macro="citations" />
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247 </tool>